I have noticed that there's now only one time of loot chest and no way to edit them. With that one Loot Chest I only get Basic rewards, so how do Loot Chests work now?

That's actually a bug. They all should be showing up but seems I missed a spot

Oh my! I came here after spending an hour manually typing all the rewards into the DefaultLoot Jason file. Only to realise I was only getting the basic tier rewards.

Is that loot chest locked to low tier?

Yes

Glad I prompted you to fix it. Thank you!

Well, I just figured out that if you set the metadata of the chest item from 0-100 that controls the rarity. I set it to 101 and it seemed to give me anything from any of the group's and abided the weighting. If you are the meta to 102 you get the item to open the GUI.

/give Player bq_standard:loot_chest 1 102

I kept forgetting to fix this till now but I've made absolutely sure that it's fixed for the next build of the expansion and included in the creative tab:

Sent the build up to CurseForge. Couldn't really find any other issues to fix in the mean time and I'm probably not going to get another chance to upload a new build for a few days.